To get tested from Bowen: you need to call them and have them send your doctor a 7 page fax that includes the forms that you need to fill out as well as what he or she needs to sign as well as instructions and requirements for your blood draw. Or your doctor can call them, but I believe they will only send the fax to your doctor.
Then get your blood drawn. I think they call it a "kit draw". If I remember correctly, you can order a kit from Bowen or just go to a lab that does kit draws (if you order a kit from Bowen you still need a doctor's order/signature on the lab req). Just make sure all the forms that Bowen faxes over are included with your blood when it gets sent off. Do not get your blood drawn on a Friday because they don't accept deliveries at Bowen on Saturdays. But the packet they send explains everything.
CDC positive: You've had a Western Blot so you're familiar with the bands. In order to be considered CDC positive you have to test positive on a certain set of bands. However, the CDC themselves admit that their stringent criteria for being "CDC positive" is only for surveillance purposes. In other words, even if you don't meet the CDC requirements you can still be positive for and have Lyme, depending on what bands react.
Bowen test: Bowen does have one standard test for Lyme, and it is a test that they developed themselves and is unique to any other known Lyme test. In layman's terms, they do *not* test for antibodies. They test for the actual antigen itself, i.e. the Borellia Burgdorferi spirochete.
Having a negative ELISA and Western Blot is very common. In fact, I was given a Western Blot at a lab other than Igenex and came up completely negative. When Igenex did it, it was an entirely different story. Many many people have tested negative on these tests, it is sad but true and makes things really difficult in trying to get a diagnosis.
Also, the only co-infection that Bowen tests for is Babesia. You will want to get tested for Erlichia and Bartonella as well.
Cracking joints: That can definitely be a Lyme symptom, but I am not sure what co-infection that might be as well. I highly recommend that you check out http://www.lymenet.org. Wonderful amazing site (as is this one!) but just about every Lyme question I have is answered by visiting that site. That, and great wisdom and help.
Good luck to you, happy to help, sorry for taking so long to respond!